Overcoming the thermodynamic equilibrium of an isomerization reaction through oxidoreductive reactions for biotransformation

Biosynthesis of a healthy natural sugar D-tagatose: advances and opportunities

D-tagatose is a natural low-calorie rare sugar with nearly the same sweet taste as sucrose. It has nutritional and functional properties of great interest for health, such as anti-diabetes, anti-caries, anti-atherosclerosis, anti-hyperlipidemia, anti-aging, improvement of intestinal microflora, etc. The production of D-tagatose from D-galactose catalyzed by an alkali suffers from limited supplies of costly feedstock (i.e., lactose) and high manufacturing costs due to harsh reaction conditions, costly separation, as well as severe degradation and pollution. In this review, we briefly present the properties of D-tagatose and its physiological effects, review the recent advances in the biosynthesis of D-tagatose from inexpensive and abundant glucans (e.g., starch) and their derivatives (e.g., D-glucose and D-fructose) and from lactose, including both academic literature and industrial patents, as well as discuss its future challenges and opportunities. The biosynthesis of D-tagatose can be catalyzed by four types of biocatalysts: enzymes, whole-cells, microbial fermentation, and in vitro multi-enzyme molecular machines. The biomanufacturing of starchy D-tagatose catalyzed by multi-enzyme molecular machines could be the most promising approach because it not only makes D-tagatose from ample starch but also surpasses the equilibria of monosaccharide isomerization reactions (e.g., D-fructose-to-D-tagatose, D-galactose-to-D-tagatose). D-tagatose as a filler for a variety of food and drinks or a key component mixed with other sweeteners would become a predominant starch-derived sweetener and partially replace high-fructose corn sirup in the future.

Eco-friendly production, separation and purification of D-tagatose and D-allulose from whey powder via one-pot whole-cells biotransformation, yeast fermentation and chromatography

Whey powder (WP), a dairy by-product with high biochemical oxygen demand (BOD) and chemical oxygen demand (COD), presents challenges due to its high production, low-value utilization, and environmental pollution. Based on the idea of turning waste into treasure, high-value use of WP was studied. Firstly, an engineered Bacillus subtilis co-expressing β-galactosidase (β-Gal) and L-arabinose isomerase (LAI) was constructed, which ultimately yielded 77.5 g/L D-tagatose from 500 g/L lactose. Subsequently, an engineered Escherichia coli co-expressing glucose isomerase (GI) and D-allulose 3-epimerase (DAE) was used together with above recombinant B. subtilis in a one-pot whole-cell biotransformation, and 29.11 g/L D-tagatose and 11.45 g/L D-allulose were derived from 200 g/L WP (equating to 140 g/L lactose) with yield of 0.29 g rare sugars/g lactose. In addition, the d-glucose, d-fructose and D-galactose in the reaction solution were removed by Saccharomyces cerevisiae S288C fermentation, and finally chromatography was used in separation of D-tagatose and D-allulose to obtain the purified products with 97.5 % and 95.0 % purities, respectively. This study showcases the eco-friendly production of D-tagatose and D-allulose from WP, with their separation and purification via yeast fermentation and chromatography successfully carried out for the first time.

Green biotechnological synthesis of rare sugars/alcohols: D-allulose, allitol, D-tagatose, L-xylulose, L-ribose

Rare sugars are paid more attention because of which have the characteristics of low calorie, low absorption and excellent physiological functions. Biotechnological synthesis of rare sugars has the advantages of being green, clean, simple and economic compared to chemical synthesis. Abundant enzymes for rare sugars biosynthesis are introduced and multienzyme cascade catalytic system (MECCS) used in biosynthesis of rare sugars is highlighted in this paper. Different biosynthesis pathways of five important rare sugars (D-allulose, allitol, D-tagatose, L-xylulose, l-ribose), mainly containing isomerization/epimerization reaction (existing thermodynamic equilibrium limitation), reduction-oxidation reaction (needing expensive cofactors) and phosphorylation-dephosphorylation reaction pathways (inherent constraint of thermodynamic equilibrium and requirement high-cost cofactors) etc., are reviewed. Furthermore, techniques of cofactor regeneration and enzyme/cell immobilization are provided. Finally, unique insights and expectations for future development in biosynthesis of rare sugars are given. This review provides a comprehensive analysis of the latest biotechnological advancements in the biosynthesis of rare sugars/alcohols, highlighting innovative multienzyme cascade catalytic systems and cofactor regeneration strategies.

Activating the d-Tagatose Production Capacity of Escherichia coli with Structural Insights into C4 Epimerase Specificity

d-Tagatose, a rare low-calorie sweetener, is ideal for beverages due to its high solubility and low viscosity. Current enzymatic production methods from d-galactose or d-galactitol are limited by reaction reversibility, affecting the yield and purity. This study demonstrates that Escherichia coli harbors a thermodynamically favorable pathway for producing d-tagatose from d-glucose via phosphorylation-epimerization-dephosphorylation steps. GatZ and KbaZ, annotated as aldolase chaperones, exhibit C4 epimerization activity, converting d-fructose-6-phosphate to d-tagatose-6-phosphate. Structural analysis reveals active site differences between these enzymes and class II aldolases, indicating functional divergence. By exploiting the strains' inability to metabolize d-tagatose, carbon starvation was applied to remove sugar byproducts. The engineered strains converted 45 g L-1 d-glucose to d-tagatose, achieving a titer of 7.3 g L-1 and a productivity of 0.1 g L-1 h-1 under test tube conditions. This approach highlights E. coli as a promising host for efficient d-tagatose production.

Construction of a multienzyme cascade reaction system and its application in D-tagatose biosynthesis

D-tagatose, a low-calorie rare sugar, has significant potential in food, medicine, cosmetics, and other industries owing to its high application value and market potential. In this study, Escherichia coli BL21 was used as the starting strain to express the β-galactosidase (β-Gal) gene-BgaB-derived from Bacillus stearothermophilus and the L-arabinose isomerase (L-AI) gene-araA-derived from Thermus sp., yielding the genetically engineered strains E. coli BL21-pET28a-BgaB and E. coli BL21-pET28a-araA. These strains synthesized D-tagatose using β-Gal and L-AI with a conversion rate of 23.73%. Based on this, we constructed a multienzyme cascade pathway comprising β-Gal, L-AI, glucose isomerase (GI), fructose kinase (FK), D-tagatose-bisphosphate aldolase (GatZ), polyphosphate kinase (PPK), and phosphatase (PGP), further enhancing D-tagatose biosynthesis. This multienzyme approach improved the conversion of the intermediate product D-glucose to D-tagatose by 3.84% compared with the dual-enzyme system. Thus, our study provides a theoretical basis and technical support for the industrial production of D-tagatose.

Engineering Saccharomyces cerevisiae for growth on xylose using an oxidative pathway

The fermentative production of valuable chemicals from lignocellulosic feedstocks has attracted considerable attention. Although Saccharomyces cerevisiae is a promising microbial host, it lacks the ability to efficiently metabolize xylose, a major component of lignocellulosic feedstocks. The xylose oxidative pathway offers advantages such as simplified metabolic regulation and fewer enzymatic steps. Specifically, the pathway involves the conversion of xylose into 2-keto-3-deoxy-xylonate, which can be channeled into two distinct pathways, the Dahms pathway and the Weimberg pathway. However, the growth of yeast on xylose as the sole carbon source through the xylose oxidative pathway has not been achieved, limiting its utilization. We successfully engineered S. cerevisiae to metabolize xylose as its sole carbon source via the xylose oxidative pathways, achieved by enhancing enzyme activities through iron metabolism engineering and rational enzyme selection. We found that increasing the supply of the iron-sulfur cluster to activate the bottleneck enzyme XylD by BOL2 disruption and tTYW1 overexpression facilitated the growth of xylose and the production of ethylene glycol at 1.5 g/L via the Dahms pathway. Furthermore, phylogenetic analysis of xylonate dehydratases led to the identification of a highly active homologous enzyme. A strain possessing the Dahms pathway with this highly active enzyme exhibited reduced xylonate accumulation. Furthermore, the introduction of enzymes based on phylogenetic tree analysis allowed for the utilization of xylose as the sole carbon source through the Weimberg pathway. This study highlights the potential of iron metabolism engineering and phylogenetic enzyme selection for the development of non-native metabolic pathways in yeast. KEY POINTS: • A 1.5 g/L ethylene glycol was produced via the Dahms pathway in S. cerevisiae. • Enzyme activation enabled growth on xylose via both the Dahms and Weimberg pathways. • Tested enzymes in this study may expand the application of xylose oxidative pathway.

Transforming monosaccharides: Recent advances in rare sugar production and future exploration

Rare sugars are defined as monosaccharides and their derivatives that do not exist in nature at all or that exist in extremely limited amounts despite being theoretically possible. At present, no comprehensive dogma has been presented regarding how and why these rare sugars have deviated from the naturally selected monosaccharides. In this minireview, we adopt a hypothesis on the origin and evolution of elementary hexoses, previously presented by one of the authors (Hirabayashi, Q Rev Biol, 1996, 71:365-380). In this scenario, monosaccharides, which constitute various kinds of glycans in nature, are assumed to have been generated by formose reactions on the prebiotic Earth (chemical evolution era). Among them, the most stable hexoses, i.e., fructose, glucose, and mannose remained accumulated. After the birth of life, the "chemical origin" saccharides thus survived were transformed into a variety of "bricolage products", which include galactose and other recognition saccharides like fucose and sialic acid through the invention of diverse metabolic pathways (biological evolution era). The remaining monosaccharides that have deviated from this scenario are considered rare sugars. If we can produce rare sugars as we wish, it is expected that various more useful biomaterials will be created by using them as raw materials. Thanks to the pioneering research of the Izumori group in the 1990's, and to a few other investigations by other groups, almost all monosaccharides including l-sugars can now be produced by combining both chemical and enzymatic approaches. After briefly giving an overview of the origin of elementary hexoses and the current state of the rare sugar production, we will look ahead to the next generation of monosaccharide research which also targets glycosides including disaccharides.

Thermostability Enhancement of Tagatose 4-Epimerase through Protein Engineering and Whole-Cell Immobilization

d-Tagatose, a rare sugar endowed with a low-calorie property, superior taste quality, and probiotic functionality, has garnered significant research attention. However, the prevailing biological production methods relying on β-galactosidase and l-arabinose isomerase face challenges including high cost and suboptimal conversion efficiency. Consequently, it is of great research significance to find efficient alternative routes for d-tagatose synthesis. Previously, Thermotoga petrophila tagaturonate 3-epimerase was modified to function as tagatose 4-epimerase (T4E) enabling the direct conversion of d-fructose to d-tagatose. In this study, T4E was further engineered through directed evolution, specifically targeting the enhancement of its thermostability for application. This endeavor yielded promising T4E variants with superiority over those of the original enzyme. T4E I430P exhibits a half-life (t1/2) at 70 °C that is 1.83-fold that of T4E, with an increased melting temperature (Tm) of 5.1 °C compared to T4E. Additionally, T4E G90S/T272A/I430P demonstrated a 21.4% increase in specific activity compared to T4E. At 70 °C, its t1/2 was 1.69-fold that of T4E, and its Tm is 2.9 °C higher than T4E. Furthermore, whole-cell immobilization integrating these engineered T4E variants into a robust biocatalytic system was employed. This innovative approach not only underscores the practical feasibility of modifying enzymes through directed evolution but also establishes a foundation for the cost-effective, large-scale production of d-tagatose.

Regulation of Metabolic Pathways to Enhance Difucosyllactose Biosynthesis in Escherichia coli

Difucosyllactose (DFL), an important kind of fucosylated human milk oligosaccharides (HMOs), has garnered considerable attention due to its excellent physiological activities in infants. Previously, we achieved de novo biosynthesis of DFL; however, substantial residual intermediates of fucosyllactoses (FL) were detected. In this study, DFL biosynthesis was optimized, and residual FL were reduced by regulating metabolic pathways. Different plasmid combinations were used to regulate gene expression, achieving an optimal flux balance between 2'-FL and DFL. The expression level of key enzyme α-1,3-fucosyltransferase (α-1,3-FT, FucTa) was then enhanced by increasing plasmid copy number and integrating fucTa gene into the chromosome. Exocytosis of 2'-FL was reduced by deleting the sugar efflux transporter setA gene, thereby minimizing residual FL. Finally, strain BSF41 produced 55.3 g/L of DFL with only 2.59 g/L of residual FL in a 5 L fermentor, representing the highest reported titer to date. This study provides an important foundation for advancing the biosynthesis of fucosylated HMOs.

Artificial Cascade Transformation Biosystem for One-Pot Biomanufacturing of Odd-Numbered Neoagarooligosaccharides and d-Tagatose through Wiser Agarose Utilization

The application of agarose oligosaccharides has garnered great attention, with their biological activities varying among different structures. However, it still meets a great bottleneck for the targeted production of odd-numbered neoagarooligosaccharides (NAOSs), such as neoagarotriose (NA3), due to the lack of one-step hydrolases. In this work, the α-agarase AgaA33 and β-galactosidase BgaD were synergistically used to prepare NA3 with agarose as a substrate. Additionally, an l-arabinose isomerase CaLAI from Clostridium acetobutylicum was characterized to valorize low-value byproducts (d-galactose) by forming d-tagatose, which exhibited good thermal stability without the need for additional metal ions. Under the optimal reaction conditions, the production of NA3 and d-galactose catalyzed by these three enzymes was 0.40 and 0.15 g/L, respectively. The artificial three-enzyme-based cascade transformation system not only achieved the highest production of NA3 until now but also allowed for the valorization of d-galactose, providing a wiser application route for agarose utilization.

A unique metabolic gene cluster regulates lactose and galactose metabolism in the yeast Candida intermedia

Lactose assimilation is a relatively rare trait in yeasts, and Kluyveromyces yeast species have long served as model organisms for studying lactose metabolism. Meanwhile, the metabolic strategies of most other lactose-assimilating yeasts remain unknown. In this work, we have elucidated the genetic determinants of the superior lactose-growing yeast Candida intermedia. Through genomic and transcriptomic analyses, we identified three interdependent gene clusters responsible for the metabolism of lactose and its hydrolysis product galactose: the conserved LAC cluster (LAC12, LAC4) for lactose uptake and hydrolysis, the conserved GAL cluster (GAL1, GAL7, and GAL10) for galactose catabolism through the Leloir pathway, and a "GALLAC" cluster containing the transcriptional activator gene LAC9, second copies of GAL1 and GAL10, and a XYL1 gene encoding an aldose reductase involved in carbon overflow metabolism. Bioinformatic analysis suggests that the GALLAC cluster is unique to C. intermedia and has evolved through gene duplication and divergence, and deletion mutant phenotyping proved that the cluster is indispensable for C. intermedia's growth on lactose and galactose. We also show that the regulatory network in C. intermedia, governed by Lac9 and Gal1 from the GALLAC cluster, differs significantly from the galactose and lactose regulons in Saccharomyces cerevisiae, Kluyveromyces lactis, and Candida albicans. Moreover, although lactose and galactose metabolism are closely linked in C. intermedia, our results also point to important regulatory differences.IMPORTANCEThis study paves the way to a better understanding of lactose and galactose metabolism in the non-conventional yeast C. intermedia. Notably, the unique GALLAC cluster represents a new, interesting example of metabolic network rewiring and likely helps to explain how C. intermedia has evolved into an efficient lactose-assimilating yeast. With the Leloir pathway of budding yeasts acting like a model system for understanding the function, evolution, and regulation of eukaryotic metabolism, this work provides new evolutionary insights into yeast metabolic pathways and regulatory networks. In extension, the results will facilitate future development and use of C. intermedia as a cell-factory for conversion of lactose-rich whey into value-added products.

Stereoselective Solid-State Synthesis of Biologically Active Cyclobutane and Dicyclobutane Isomers via Conformation Blocking and Transference

Conformations in the solid state are typically fixed during crystallization. Transference of "frozen" C=C conformations in 3,5-bis((E)-2-(pyridin-4-yl)vinyl)methylbenzene (CH3-3,5-bpeb) by photodimerization selectively yielded cyclobutane and dicyclobutane isomers, one of which (Isomer 2) exhibited excellent in vitro anti-cancer activity towards T-24, 7402, MGC803, HepG-2, and HeLa cells.

Enzymatic biosynthesis of D-galactose derivatives: Advances and perspectives

D-Galactose derivatives, including galactosyl-conjugates and galactose-upgrading compounds, provide various physiological benefits and find applications in industries such as food, cosmetics, feed, pharmaceuticals. Many research on galactose derivatives focuses on identification, characterization, development, and mechanistic aspects of their physiological function, providing opportunities and challenges for the development of practical approaches for synthesizing galactose derivatives. This study focuses on recent advancements in enzymatic biosynthesis of galactose derivatives. Various strategies including isomerization, epimerization, transgalactosylation, and phosphorylation-dephosphorylation were extensively discussed under the perspectives of thermodynamic feasibility, theoretical yield, cost-effectiveness, and by-product elimination. Specifically, the enzymatic phosphorylation-dephosphorylation cascade is a promising enzymatic synthesis route for galactose derivatives because it can overcome the thermodynamic equilibrium of isomerization and utilize cost-effective raw materials. The study also elucidates the existing challenges and future trends in enzymatic biosynthesis of galactose derivatives. Collectively, this review provides a real-time summary aimed at promoting the practical biosynthesis of galactose derivatives through enzymatic catalysis.

A hybrid photocatalytic system enables direct glucose utilization for methanogenesis

Integration of methanogenic archaea with photocatalysts presents a sustainable solution for solar-driven methanogenesis. However, maximizing CH4 conversion efficiency remains challenging due to the intrinsic energy conservation and strictly restricted substrates of methanogenic archaea. Here, we report a solar-driven biotic-abiotic hybrid (biohybrid) system by incorporating cadmium sulfide (CdS) nanoparticles with a rationally designed methanogenic archaeon Methanosarcina acetivorans C2A, in which the glucose synergist protein and glucose kinase, an energy-efficient route for glucose transport and phosphorylation from Zymomonas mobilis, were implemented to facilitate nonnative substrate glucose for methanogenesis. We demonstrate that the photo-excited electrons facilitate membrane-bound electron transport chain, thereby augmenting the Na+ and H+ ion gradients across membrane to enhance adenosine triphosphate (ATP) synthesis. Additionally, this biohybrid system promotes the metabolism of pyruvate to acetyl coenzyme A (AcCoA) and inhibits the flow of AcCoA to the tricarboxylic acid (TCA) cycle, resulting in a 1.26-fold augmentation in CH4 production from glucose-derived carbon. Our results provide a unique strategy for enhancing methanogenesis through rational biohybrid design and reprogramming, which gives a promising avenue for sustainably manufacturing value-added chemicals.

An artificial multienzyme cascade for the whole-cell synthesis of rare ketoses from glycerol

PURPOSE

In our previous study, we constructed a one-pot multi-enzyme system for rare ketoses synthesis based on L-rhamnulose-1-phosphate aldolase (RhaD) from accessible glycerol in vitro. To eliminate tedious purification of enzymes, a facile Escherichia coli whole-cell cascade platform was established in this study.

METHODS

To enhance the conversion rate, the reaction conditions, substrate concentrations and expressions of related enzymes were extensively optimized.

RESULTS

The biosynthetic route for the cascade synthesis of rare ketoses in whole cells was successfully constructed and three rare ketoses including D-allulose, D-sorbose and L-fructose were produced using glycerol and D/L-glyceraldehyde (GA). Under optimized conditions, the conversion rates of rare ketoses were 85.0% and 93.0% using D-GA and L-GA as the receptor, respectively. Furthermore, alditol oxidase (AldO) was introduced to the whole-cell system to generate D-GA from glycerol, and the total production yield of D-sorbose and D-allulose was 8.2 g l-1 only from the sole carbon source glycerol.

CONCLUSION

This study demonstrates a feasible and cost-efficient method for rare sugars synthesis and can also be applied to the green synthesis of other value-added chemicals from glycerol.

Recent Advances in the Biosynthesis of Natural Sugar Substitutes in Yeast

Natural sugar substitutes are safe, stable, and nearly calorie-free. Thus, they are gradually replacing the traditional high-calorie and artificial sweeteners in the food industry. Currently, the majority of natural sugar substitutes are extracted from plants, which often requires high levels of energy and causes environmental pollution. Recently, biosynthesis via engineered microbial cell factories has emerged as a green alternative for producing natural sugar substitutes. In this review, recent advances in the biosynthesis of natural sugar substitutes in yeasts are summarized. The metabolic engineering approaches reported for the biosynthesis of oligosaccharides, sugar alcohols, glycosides, and rare monosaccharides in various yeast strains are described. Meanwhile, some unresolved challenges in the bioproduction of natural sugar substitutes in yeast are discussed to offer guidance for future engineering.

Biocatalytic Foams from Microdroplet-Formulated Self-Assembling Enzymes

Industrial biocatalysis plays an important role in the development of a sustainable economy, as enzymes can be used to synthesize an enormous range of complex molecules under environmentally friendly conditions. To further develop the field, intensive research is being conducted on process technologies for continuous flow biocatalysis in order to immobilize large quantities of enzyme biocatalysts in microstructured flow reactors under conditions that are as gentle as possible in order to realize efficient material conversions. Here, monodisperse foams consisting almost entirely of enzymes covalently linked via SpyCatcher/SpyTag conjugation are reported. The biocatalytic foams are readily available from recombinant enzymes via microfluidic air-in-water droplet formation, can be directly integrated into microreactors, and can be used for biocatalytic conversions after drying. Reactors prepared by this method show surprisingly high stability and biocatalytic activity. The physicochemical characterization of the new materials is described and exemplary applications in biocatalysis are shown using two-enzyme cascades for the stereoselective synthesis of chiral alcohols and the rare sugar tagatose.

Efficient production of d-tagatose via DNA scaffold mediated oxidoreductases assembly in vivo from whey powder

Among the emerging sweeteners, d-tagatose occupies a significant niche due to its low calorific value, antidiabetic property and growth promoting effects on intestinal probiotics. Recently, the main approach for d-tagatose biosynthesis is l-arabinose isomerase-based isomerization reaction from galactose, which shows relatively low conversion rate because of unfavorable thermodynamic equilibria. Herein, oxidoreductases, d-xylose reductase and galactitol dehydrogenase, together with endogenous β-galactosidase were employed to catalyze the biosynthesis of d-tagatose from lactose with a yield of 0.282 g/g in Escherichia coli. Then, a deactivated CRISPR-associated (Cas) proteins-based DNA scaffold system was developed, which were proved to be efficient for assembling the oxidoreductases in vivo and got a 1.44-folds increase in d-tagatose titer and yield. Further, by employing d-xylose reductase with higher galactose affinity and activity, as well as overexpressing pntAB genes, the d-tagatose yield from lactose (0.484 g/g) increased to 92.0 % of the theoretical value, 1.72-times as that of original strain. Finally, whey powder, a lactose-rich food by-product, was bifunctionally utilized as an inducer and substrate. In the 5 L bioreactor, d-tagatose titer reached 32.3 g/L with little galactose detected, and the yield from lactose approached 0.402 g/g, which was the highest from waste biomass in the literature. The strategies used here might provide new insights into the biosynthesis of d-tagatose in future.

Engineering Pheromone-Mediated Quorum Sensing with Enhanced Response Output Increases Fucosyllactose Production in Saccharomyces cerevisiae

Engineering dynamic control of gene expression is desirable because many engineered functions interfere with endogenous cellular processes that have evolved to facilitate growth and survival. Minimizing conflict between growth and production phases can therefore improve product titers in microbial cell factories. We developed an autoinduced gene expression system by rewiring the Saccharomyces cerevisiae pheromone response pathway. To ameliorate growth reduction due to the early onset response at low population densities, α-pheromone of Kluyveromyces lactis (Kα) instead of S. cerevisiae (Sα) was expressed in mating type "a" yeast. Kα-induced expression of pathway genes was further enhanced by the transcriptional activator Gal4p expressed under the control of the pheromone-responsive FUS1 promoter (P_fus1). As a demonstration, the engineered circuit combined with the deletion of the endogenous galactose metabolic pathway genes was applied to the production of human milk oligosaccharides, 2'-fucosyllactose (2'-FL) and 3-fucosllactose (3-FL). The engineered strains produced 3.37 g/L 2'-FL and 2.36 g/L 3-FL on glucose with a volumetric productivity of 0.14 and 0.03 g/L·h^-1 in batch flask cultivation, respectively. These represented 147 and 153% increases over the control strains on galactose wherein the respective pathway genes are expressed under GAL promoters only. Further fed-batch fermentation achieved titers of 32.05 and 20.91 g/L for 2' and 3-FL, respectively. The genetic program developed here thus represents a promising option for implementing dynamic regulation in yeast and could be used for the production of biochemicals that may place a heavy metabolic burden on cell growth.

Rare sugars: metabolic impacts and mechanisms of action: a scoping review

Food manufacturers are under increasing pressure to limit the amount of free sugars in their products. Many have reformulated products to replace sucrose, glucose and fructose with alternative sweeteners, but some of these have been associated with additional health concerns. Rare sugars are ‘monosaccharides and their derivatives that hardly exist in nature’, and there is increasing evidence that they could have health benefits. This review aimed to scope the existing literature in order to identify the most commonly researched rare sugars, to ascertain their proposed health benefits, mechanisms of action and potential uses and to highlight knowledge gaps. A process of iterative database searching identified fifty-five relevant articles. The reported effects of rare sugars were noted, along with details of the research methodologies conducted. Our results indicated that the most common rare sugars investigated are d-psicose and d-tagatose, with the potential health benefits divided into three topics: glycaemic control, body composition and CVD. All the rare sugars investigated have the potential to suppress postprandial elevation of blood glucose and improve glycaemic control in both human and animal models. Some animal studies have suggested that certain rare sugars may also improve lipid profiles, alter the gut microbiome and reduce pro-inflammatory cytokine expression. The present review demonstrates that rare sugars could play a role in reducing the development of obesity, type 2 diabetes and/or CVD. However, understanding of the mechanisms by which rare sugars may exert their effects is limited, and their effectiveness when used in reformulated products is unknown.

Metabolic engineering of oleaginous yeast Rhodotorula toruloides for overproduction of triacetic acid lactone

The plant‐sourced polyketide triacetic acid lactone (TAL) has been recognized as a promising platform chemical for the biorefinery industry. However, its practical application was rather limited due to low natural abundance and inefficient cell factories for biosynthesis. Here, we report the metabolic engineering of oleaginous yeast Rhodotorula toruloides for TAL overproduction. We first introduced a 2‐pyrone synthase gene from Gerbera hybrida (GhPS) into R. toruloides and investigated the effects of different carbon sources on TAL production. We then systematically employed a variety of metabolic engineering strategies to increase the flux of acetyl‐CoA by enhancing its biosynthetic pathways and disrupting its competing pathways. We found that overexpression of ATP‐citrate lyase (ACL1) improved TAL production by 45% compared to the GhPS overexpressing strain, and additional overexpression of acetyl‐CoA carboxylase (ACC1) further increased TAL production by 29%. Finally, we characterized the resulting strain I12‐ACL1‐ACC1 using fed‐batch bioreactor fermentation in glucose or oilcane juice medium with acetate supplementation and achieved a titer of 28 or 23 g/L TAL, respectively. This study demonstrates that R. toruloides is a promising host for the production of TAL and other acetyl‐CoA‐derived polyketides from low‐cost carbon sources.

Synthetic biology: a new frontier in food production

Concerns regarding food security arise from population growth, global warming, and reduction in arable land. With advances in synthetic biology, food production by microbes is considered to be a promising alternative that would allow rapid food production in an environmentally friendly manner. Moreover, synthetic biology can be adopted to the production of healthier or specifically designed food ingredients (e.g., high-value proteins, lipids, and vitamins) and broaden the utilization of feedstocks (e.g., methanol and CO₂), thereby offering potential solutions to high-quality food and the greenhouse effect. We first present how synthetic biology can facilitate the microbial production of various food components, and then discuss feedstock availability enabled by synthetic biology. Finally, we illustrate trends and key challenges in synthetic biology-driven food production.

D-allulose, a versatile rare sugar: recent biotechnological advances and challenges

D-Allulose is the C-3 epimer of D-fructose, and widely regarded as a promising substitute for sucrose. It's an excellent low-calorie sweetener, with 70% sweetness of sucrose, 0.4 kcal/g dietary energy, and special physiological functions. It has been approved as GRAS by the U.S. Food and Drug Administration, and is allowed to be excluded from total and added sugar counts on the food labels. Therefore, D-allulose gradually attracts more public attention. Owing to scarcity in nature, the bioproduction of D-allulose by using ketose 3-epimerase (KEase) has become the research hotspot. Herein, we give a summary of the physicochemical properties, physiological function, applications, and the chemical and biochemical synthesis methods of D-allulose. In addition, the recent progress in the D-allulose bioproduction using KEases, and the possible solutions for existing challenges in the D-allulose industrial production are comprehensively discussed, focusing on the molecular modification, immobilization, food-grade expression, utilizing low-cost biomass as feedstock, overcoming thermodynamic limitation, as well as the downstream separation and purification. Finally, Prospects for further development are also proposed.

Recent advances in (chemo)enzymatic cascades for upgrading bio-based resources

Developing (chemo)enzymatic cascades is very attractive for green synthesis, because they streamline multistep synthetic processes. In this Feature Article, we have summarized the recent advances in in vitro or whole-cell cascade reactions with a focus on the use of renewable bio-based resources as starting materials. This includes the synthesis of rare sugars (such as ketoses, L-ribulose, D-tagatose, myo-inositol or aminosugars) from readily available carbohydrate sources (cellulose, hemi-cellulose, starch), in vitro enzyme pathways to convert glucose to various biochemicals, cascades to convert 5-hydroxymethylfurfural and furfural obtained from lignin or xylose into novel precursors for polymer synthesis, the syntheses of phenolic compounds, cascade syntheses of aliphatic and highly reduced chemicals from plant oils and fatty acids, upgrading of glycerol or ethanol as well as cascades to transform natural L-amino acids into high-value (chiral) compounds. In several examples these processes have demonstrated their efficiency with respect to high space-time yields and low E-factors enabling mature green chemistry processes. Also, the strengths and limitations are discussed and an outlook is provided for improving the existing and developing new cascades.

Investigating the role of the transcriptional regulator Ure2 on the metabolism of Saccharomyces cerevisiae: a multi-omics approach

Ure2 regulates nitrogen catabolite repression in Saccharomyces cerevisiae. Deletion of URE2 induces a physiological state mimicking the nitrogen starvation and autophagic responses. Previous work has shown that deletion of URE2 increases the fermentation rate of some wine-producing strains of S. cerevisiae. In this work, we investigated the effect of URE2 deletion (ΔURE2) on the metabolism of S. cerevisiae. During growth on glucose, the ΔURE2 mutant grew at a 40% slower rate than the wild type; however, it produced ethanol at a 31% higher rate. To better under the behavior of this mutant, we performed transcriptomics and metabolomics. Analysis of the RNA sequencing results and metabolite levels indicates that the mutant strain exhibited characteristics of both nitrogen starvation and autophagy, including the upregulation of allantoin, urea, and amino acid uptake and utilization pathways and selective autophagic machinery. In addition, pyruvate decarboxylase and alcohol dehydrogenase isoforms were expressed at higher rates than the wild type. The mutant also accumulated less trehalose and glycogen, and produced more lipids. The induction of a nitrogen starvation-like state and increase in lipid production in nitrogen-rich conditions suggest that URE2 may be a promising target for metabolic engineering in S. cerevisiae and other yeasts for the production of lipids and lipid-derived compounds. KEY POINTS: • Deletion of URE2 increases ethanol and lipid production in Saccharomyces cerevisiae. • Deletion of URE2 reduces glycogen and trehalose production. • Metabolic changes mimic nitrogen starvation and autophagic response.

Improving the enzyme property of D-allulose 3-epimerase from a thermophilic organism of Halanaerobium congolense through rational design

The rare sugar d-allulose is an attractive sucrose substitute due to its sweetness and ultra-low caloric value. It can be produced from D-fructose using d-allulose 3-epimerase (DAE) as the biocatalyst. However, most of the reported DAEs show low catalytic efficiency and poor thermostability, which limited their further use in food industrial. Here, a putative d-allulose 3-epimerase from a thermophilic organism of Halanaerobium congolense (HcDAE) was characterized, showing optimal activity at pH 8.0 and 70 °C in the presence of Mg²⁺. Saturation mutagenesis of Y7, C66, and I108, the putative residues responsible for substrate recognition at the O-4, -5, and -6 atoms of D-fructose was performed, and it yielded the triple mutant Y7H/C66L/I108A with improved activity toward D-fructose (345 % of wild-type enzyme). The combined mutant Y7H/C66L/I108A/R156C/K260C exhibited a half-half (t_1/2) of 5.2 h at 70 °C and an increase of the T_m value by 6.5 °C due to the introduction of disulfide bridges between intersubunit with increased interface interactions. The results indicate that mutants could be used as industrial biocatalysts for d-allulose production.

Efficient bioconversion of high-concentration d-fructose into d-mannose by a novel N-acyl-d-glucosamine 2-epimerase from Thermobifida halotolerans

A novel N-acyl-d-glucosamine 2-epimerase ThMI exhibits high mannose isomerase activity with a maximum bioconversion ratio of 35.8% in 500 g L⁻¹d-fructose. Whole-cell biocatalyst produced 157 g L⁻¹d-mannose from 500 g L⁻¹d-fructose in 60 min.

Supramolecular-induced regiocontrol over the photochemical [4 + 4] cyclodimerization of NHC- or azole-substituted anthracenes

Thanks to the impressive control that microenvironments within enzymes can have over substrates, many biological reactions occur with high regio- and stereoselectivity. However, comparable regio- and stereoselectivity is extremely difficult to achieve for many types of reactions, particularly photochemical cycloaddition reactions in homogeneous solutions. Here, we describe a supramolecular templating strategy that enables photochemical [4 + 4] cycloaddition of 2,6-difunctionalized anthracenes with unique regio- and stereoselectivity and reactivity using a concept known as the supramolecular approach. The reaction of 2,6-azolium substituted anthracenes H₄-L(PF₆)₂ (L = 1a–1c) with Ag₂O yielded complexes anti-[Ag₂L₂](PF₆)₄ featuring an antiparallel orientation of the anthracene groups. Irradiation of complexes anti-[Ag₂L₂](PF₆)₄ proceeded under [4 + 4] cycloaddition linking the two anthracene moieties to give cyclodimers anti-[Ag₂(2)](PF₆)₂. Reaction of 2,6-azole substituted anthracenes with a dinuclear complex [Cl-Au-NHC–NHC-Au-Cl] yields tetranuclear assemblies with the anthracene moieties oriented in syn-fashion. Irradiation and demetallation gives a [4 + 4] syn-photodimer of two anthracenes. The stereoselectivity of the [4 + 4] cycloaddition between two anthracene moieties is determined by their orientation in the metallosupramolecular assemblies.

A supramolecular templating strategy that enables the photochemical [4 + 4] cycloaddition of 2,6-difunctionalized anthracene derivatives with unique stereoselectivity has been developed based on metal-NHC units.

Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production

Many platform chemicals can be produced from renewable biomass by microorganisms, with organic acids making up a large fraction. Intolerance to the resulting low pH growth conditions, however, remains a challenge for the industrial production of organic acids by microorganisms. Issatchenkia orientalis SD108 is a promising host for industrial production because it is tolerant to acidic conditions as low as pH 2.0. With the goal to systematically assess the metabolic capabilities of this non-model yeast, we developed a genome-scale metabolic model for I. orientalis SD108 spanning 850 genes, 1826 reactions, and 1702 metabolites. In order to improve the model’s quantitative predictions, organism-specific macromolecular composition and ATP maintenance requirements were determined experimentally and implemented. We examined its network topology, including essential genes and flux coupling analysis and drew comparisons with the Yeast 8.3 model for Saccharomyces cerevisiae. We explored the carbon substrate utilization and examined the organism’s production potential for the industrially-relevant succinic acid, making use of the OptKnock framework to identify gene knockouts which couple production of the targeted chemical to biomass production. The genome-scale metabolic model iIsor850 is a data-supported curated model which can inform genetic interventions for overproduction.

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Genome-scale metabolic model iIsor850 describes metabolism of I. orientalis SD108.

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Customized biomass reaction highlights differences with S. cerevisiae.

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Chemostat data elucidate growth-associated ATP maintenance.

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Substrate utilization and CRISPR/Cas9 gene knockout phenotypes validate model.

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Model pinpoints candidate gene deletions coupling succinic acid production to growth.

Biological upgrading of 3,6-anhydro-L-galactose from agarose to a new platform chemical

Recently, the utilization of renewable biomass instead of fossil fuels for producing fuels and chemicals is receiving much attention due to the global climate change. Among renewable biomass, marine algae are gaining importance as third generation biomass feedstocks owing to their advantages over lignocellulose. Particularly, red macroalgae have higher carbohydrate contents and simpler carbohydrate compositions than other marine algae. In red macroalgal carbphydrates, 3,6-anhydro-L-galactose (AHG) is the main sugar composing agarose along with D-galactose. However, AHG is not a common sugar and is chemically unstable. Thus, not only AHG but also red macroalgal biomass itself cannot be efficiently converted or utilized. Here, we biologically upgraded AHG to a new platform chemical, its sugar alcohol form, 3,6-anhydro-l-galactitol (AHGol), an anhydrohexitol. To accomplish this, we devised an integrated process encompassing a chemical hydrolysis process for producing agarobiose (AB) from agarose and a biological process for converting AB to AHGol using metabolically engineered Saccharomyces cerevisiae to efficiently produce AHGol from agarose with high titers and yields. AHGol was also converted to an intermediate chemical for plastics, isosorbide. To our knowledge, this is the first demonstration of upgrading a red macroalgal biomass component to a platform chemical via a new biological route, by using an engineered microorganism.

One-Pot Multienzyme Synthesis of Rare Ketoses from Glycerol

A facile approach is introduced here for the synthesis of rare ketoses from glycerol and d-/l-glyceraldehyde (d-/l-GA). The reactions were carried out in a one-pot multienzyme fashion in which the only carbon source is glycerol. In the enzymatic cascade, glycerol is phosphorylated and then oxidized at C2 to afford dihydroxyacetone phosphate (DHAP), the key donor for enzymatic aldol reaction. Meanwhile, the primary alcohol of glycerol is also oxidized to give the acceptor molecule GA in situ (d- or l-isomer could be formed stereospecifically with either alditol oxidase or horse liver alcohol dehydrogenase). Different DHAP-dependent aldolases were used to generate the aldol adducts (rare ketohexose phosphates) with various stereoconfigurations and diastereomeric ratios. It is worth noting that the enzyme that catalyzes the phosphorylation reaction in the first step could also help recycle the phosphate in the last step to provide free rare sugar molecules. This study provides a useful method for rare ketose synthesis on a 100 mg to g scale, starting from relatively inexpensive materials which solved the problem of supplying both glycerol 3-phosphate and GA in our previous work. It also demonstrates an example of green synthesis due to highly efficient carbon usage and recycling of cofactors.

A genetic toolbox for metabolic engineering of Issatchenkia orientalis

The nonconventional yeast Issatchenkia orientalis can grow under highly acidic conditions and has been explored for production of various organic acids. However, its broader application is hampered by the lack of efficient genetic tools to enable sophisticated metabolic manipulations. We recently constructed an episomal plasmid based on the autonomously replicating sequence (ARS) from Saccharomyces cerevisiae (ScARS) in I. orientalis and developed a CRISPR/Cas9 system for multiplexed gene deletions. Here we report three additional genetic tools including: (1) identification of a 0.8 kb centromere-like (CEN-L) sequence from the I. orientalis genome by using bioinformatics and functional screening; (2) discovery and characterization of a set of constitutive promoters and terminators under different culture conditions by using RNA-Seq analysis and a fluorescent reporter; and (3) development of a rapid and efficient in vivo DNA assembly method in I. orientalis, which exhibited ~100% fidelity when assembling a 7 kb-plasmid from seven DNA fragments ranging from 0.7 kb to 1.7 kb. As proof of concept, we used these genetic tools to rapidly construct a functional xylose utilization pathway in I. orientalis.

Galactose to tagatose isomerization at moderate temperatures with high conversion and productivity

There are many industrially-relevant enzymes that while active, are severely limited by thermodynamic, kinetic, or stability issues (isomerases, lyases, transglycosidases). In this work, we study Lactobacillus sakeil-arabinose isomerase (LsLAI) for d-galactose to d-tagatose isomerization—that is limited by all three reaction parameters. The enzyme demonstrates low catalytic efficiency, low thermostability at temperatures > 40 °C, and equilibrium conversion < 50%. After exploring several strategies to overcome these limitations, we show that encapsulating LsLAI in gram-positive Lactobacillus plantarum that is chemically permeabilized enables reactions at high rates, high conversions, and elevated temperatures. In a batch process, this system enables ~ 50% conversion in 4 h starting with 300 mM galactose (an average productivity of 37 mM h⁻¹), and 85% conversion in 48 h. We suggest that such an approach may be invaluable for other enzymatic processes that are similarly kinetically-, thermodynamically-, and/or stability-limited.

Production of tagatose, a sugar substitute, by isomerization of galactose suffers from unfavorable enzymatic kinetics, low enzyme stability, and low equilibrium constant. Here, the authors simultaneously overcome these limitations by encapsulating l-arabinose isomerase in permeabilized Lactobacillus plantarum.

Vitamin A Production by Engineered Saccharomyces cerevisiae from Xylose via Two-Phase in Situ Extraction

Vitamin A is an essential human micronutrient and plays critical roles in vision, reproduction, immune system, and skin health. Current industrial methods for the production of vitamin A rely on chemical synthesis from petroleum-derived substrates, such as acetone and acetylene. Here, we developed a biotechnological method for production of vitamin A from an abundant and nonedible sugar. Specifically, we engineered Saccharomyces cerevisiae to produce vitamin A from xylose-the second most abundant sugar in plant cell wall hydrolysates-by introducing a β-carotene biosynthetic pathway, and a gene coding for β-carotene 15,15'-dioxygenase (BCMO) into a xylose-fermenting S. cerevisiae. The resulting yeast strain produced vitamin A from xylose at a titer 4-fold higher than from glucose. When a two-phase in situ extraction strategy with dodecane or olive oil as an extractive agent was employed, vitamin A production improved additional 2-fold. Furthermore, a xylose fed-batch fermentation with dodecane in situ extraction achieved a final titer of 3350 mg/L vitamin A, which consisted of retinal (2094 mg/L) and retinol (1256 mg/L). These results suggest that potential limiting factors of vitamin A production in yeast, such as insufficient supply of isoprenoid precursors, and limited intracellular storage capacity, can be effectively addressed by using xylose as a carbon source, and two-phase in situ extraction. The engineered S. cerevisiae and fermentation strategies described in this study might contribute to sustainable and economic production of vitamin A, and vitamin A-enriched bioproducts from renewable biomass.

Production of galactitol from galactose by the oleaginous yeast Rhodosporidium toruloides IFO0880

BACKGROUND

Sugar alcohols are commonly used as low-calorie sweeteners and can serve as potential building blocks for bio-based chemicals. Previous work has shown that the oleaginous yeast Rhodosporidium toruloides IFO0880 can natively produce arabitol from xylose at relatively high titers, suggesting that it may be a useful host for sugar alcohol production. In this work, we explored whether R. toruloides can produce additional sugar alcohols.

RESULTS

Rhodosporidium toruloides is able to produce galactitol from galactose. During growth in nitrogen-rich medium, R. toruloides produced 3.2 ± 0.6 g/L, and 8.4 ± 0.8 g/L galactitol from 20 to 40 g/L galactose, respectively. In addition, R. toruloides was able to produce galactitol from galactose at reduced titers during growth in nitrogen-poor medium, which also induces lipid production. These results suggest that R. toruloides can potentially be used for the co-production of lipids and galactitol from galactose. We further characterized the mechanism for galactitol production, including identifying and biochemically characterizing the critical aldose reductase. Intracellular metabolite analysis was also performed to further understand galactose metabolism.

CONCLUSIONS

Rhodosporidium toruloides has traditionally been used for the production of lipids and lipid-based chemicals. Our work demonstrates that R. toruloides can also produce galactitol, which can be used to produce polymers with applications in medicine and as a precursor for anti-cancer drugs. Collectively, our results further establish that R. toruloides can produce multiple value-added chemicals from a wide range of sugars.